fix sample sheet validation (#2806)(patch)

## Description
As described in  #2804, sample sheet validation does not take into account the bcl converter of the flow cell.


### Added

- This PR adds a check inside the method `validate_sample_sheet` of the class `FlowCellDirectoryData` that compares the sample sheet type extracted from the sample sheet itself and the bcl converter of the `FlowCellDirectoryData`. If they don't match, it fails the validation and informs this mismatch in the logs as a warning.

cg/cli/demultiplex/demux.py

@@ -59,7 +59,8 @@ def demultiplex_all(context: CGConfig, flow_cells_directory: click.Path, dry_run
 
         if not flow_cell.validate_sample_sheet():
             LOG.warning(
-                f"Malformed sample sheet. Run cg demultiplex samplesheet validate {flow_cell.sample_sheet_path}",
+                "Malformed sample sheet. "
+                f"Run cg demultiplex sample sheet validate {flow_cell.sample_sheet_path}",
             )
             continue
 

cg/models/flow_cell/flow_cell.py

@@ -8,8 +8,12 @@
 from pydantic import ValidationError
 from typing_extensions import Literal
 
-from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_sample_sheet_from_file
+from cg.apps.demultiplex.sample_sheet.read_sample_sheet import (
+    get_sample_sheet_from_file,
+    get_sample_type,
+)
 from cg.apps.demultiplex.sample_sheet.sample_models import (
+    FlowCellSample,
     FlowCellSampleBcl2Fastq,
     FlowCellSampleBCLConvert,
 )
@@ -36,6 +40,10 @@
     Sequencers.NOVASEQ: RunParametersNovaSeq6000,
     Sequencers.NOVASEQX: RunParametersNovaSeqX,
 }
+SAMPLE_MODEL_TO_BCL_CONVERTER: dict[Type[FlowCellSample], str] = {
+    FlowCellSampleBCLConvert: BclConverter.DRAGEN,
+    FlowCellSampleBcl2Fastq: BclConverter.BCL2FASTQ,
+}
 
 
 class FlowCellDirectoryData:
@@ -213,6 +221,16 @@ def sample_sheet_exists(self) -> bool:
 
     def validate_sample_sheet(self) -> bool:
         """Validate if sample sheet is on correct format."""
+        sample_type_from_sample_sheet: Type[FlowCellSample] = get_sample_type(
+            self.sample_sheet_path
+        )
+        if SAMPLE_MODEL_TO_BCL_CONVERTER[sample_type_from_sample_sheet] != self.bcl_converter:
+            LOG.warning(
+                f"Detected {SAMPLE_MODEL_TO_BCL_CONVERTER[sample_type_from_sample_sheet]} sample "
+                f"sheet for {self.bcl_converter} flow cell. "
+                "Generate the correct sample sheet or use the correct bcl converter."
+            )
+            return False
         try:
             get_sample_sheet_from_file(self.sample_sheet_path)
         except (SampleSheetError, ValidationError) as error:

tests/cli/demultiplex/test_demultiplex_flowcell.py

@@ -10,13 +10,9 @@
 from cg.meta.demultiplex.housekeeper_storage_functions import add_sample_sheet_path_to_housekeeper
 from cg.models.cg_config import CGConfig
 from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
-from tests.meta.demultiplex.conftest import (
-    tmp_flow_cell_demux_base_path,
-    tmp_flow_cell_run_base_path,
-)
 
 
-def test_demultiplex_flow_cell_dry_run(
+def test_demultiplex_bcl2fastq_flow_cell_dry_run(
     cli_runner: testing.CliRunner,
     tmp_flow_cells_directory_ready_for_demultiplexing_bcl2fastq: Path,
     demultiplexing_context_for_demux: CGConfig,
@@ -26,7 +22,8 @@ def test_demultiplex_flow_cell_dry_run(
 
     # GIVEN that all files are present for demultiplexing
     flow_cell: FlowCellDirectoryData = FlowCellDirectoryData(
-        tmp_flow_cells_directory_ready_for_demultiplexing_bcl2fastq
+        tmp_flow_cells_directory_ready_for_demultiplexing_bcl2fastq,
+        bcl_converter=BclConverter.BCL2FASTQ,
     )
     add_sample_sheet_path_to_housekeeper(
         flow_cell_directory=tmp_flow_cells_directory_ready_for_demultiplexing_bcl2fastq,
@@ -45,7 +42,12 @@ def test_demultiplex_flow_cell_dry_run(
     # WHEN starting demultiplexing from the CLI with dry run flag
     result: testing.Result = cli_runner.invoke(
         demultiplex_flow_cell,
-        [str(tmp_flow_cells_directory_ready_for_demultiplexing_bcl2fastq), "--dry-run"],
+        [
+            str(tmp_flow_cells_directory_ready_for_demultiplexing_bcl2fastq),
+            "--dry-run",
+            "-b",
+            "bcl2fastq",
+        ],
         obj=demultiplexing_context_for_demux,
     )